Patients and methods: A retrospective analysis of 112 patients who underwent microperc surgery between December 2012 and April 2014 was performed. Patients were evaluated in two groups according to whether the presence of hydronephrosis. Stone size and location, fluoroscopy and operation time, stone-free rates and patient-related parameters were prospectively recorded into a centralized computer-generated system. Purpose: To evaluate the effects of presence of hydronephrosis on micropercutaneous nephrolithotomy (micro-PNL) surgery. Results: A total of 58 patients in Group 1 with hydronephrosis and 54 patients in Group 2 with no hydronephrosis were analyzed. There was no statistically significant difference in terms of stone sizes and body mass indexes (BMI) in comparison of groups (155.2 ± 93.06 vs. 143.70 ± 70.77 mm2, p = 0.856 and 27.6 ± 4.2 vs. 26.7 ± 3.2 kg/m2, p = 0.625). The success rates were similar (91.3 vs. 92.5 %, p = 0.341). While the mean operation time and fluoroscopy time in Group 1 were 44.2 ± 23.62 min and 105.3 ± 47 s, it was 38.8 ± 26.4 min and 112.53 ± 68.3 s in Group 2, but there was no statistical difference in comparison of both groups. The mean attempts of percutan puncture were 1.35 ± 0.47 in Group 1 and 1.76 ± 0.31 in Group 2 (p = 0.185). We also found no statistical differences regarding mean hemoglobin change and hospitalization time, respectively (p = 0.685 and p = 0753). In comparison of grades of hydronephrosis, there was no statistically significant difference in subgroups analysis. Conclusions: The presence of hydronephrosis does not affect success rates and operative time in micro-PNL procedures significantly. Micropercutaneous nephrolithotomy is technically feasible and efficacious both in hydronephrotic and non-hydronephrotic kidneys.